So this was an hilarious case of reference counting.
There I was, developing my Perl Catalyst app. I migrate to gitlab like all the other cool kids. I move the original development directory to .bak like a good boy.
But, my plackup is still running and because reference counting, the open files are all still there so I was still happily running. I check out the gitlab version, make changes and NOTHING HAPPENS. Until finally the penny drops, I quit the original, now renamed directory and re-enter the correct one.
Suddenly everything works and hilarity ensues.